Package: CoreGx 2.9.0
Benjamin Haibe-Kains
CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Authors:
CoreGx_2.9.0.tar.gz
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CoreGx.pdf |CoreGx.html✨
CoreGx/json (API)
NEWS
| # Install 'CoreGx' in R: |
| install.packages('CoreGx', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- clevelandSmall_cSet - Cleaveland_mut RadioSet subsetted and cast as CoreSet
- exampleDataMapper - Example LongTableDataMapper
- merckLongTable - Merck Drug Combination Data LongTable
- nci_TRE_small - NCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset
On BioConductor:CoreGx-2.9.0(bioc 3.20)CoreGx-2.8.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:f467415a8c
Exports:..all_equals.collapse.distancePointLine.distancePointSegment.dmedncauchys.dmednnormals.edmedncauchys.edmednnormals.error.errorMsg.examineGOF.fitCurve.fitCurve2.formatMessage.funContext.getSupportVec.intersectList.length_unique.linInd.list_unique.magnitude.matInd.meshEval.meshEval2.message.multinom.parseToRoxygen.patternSearch.patternSearch2.pmedncauchys.pmednnormals.reformatData.residual.rmedncauchys.rmednnormals.S4MethodContext.sanitizeInput.stripWhiteSpace.summarizeMolecularNumbers.symSetDiffList.unionList.warning.warnMsgaggregateaggregate2amccannotationannotation<-asas.long.tableassayassay<-assayColsassayIndexassayKeysassayMapassayMap<-assayNamesassaysassays<-buildComboProfilesbuildLongTablecallingWaterfallcardinalitycellInfocellInfo<-cellNamescellNames<-checkColumnCardinalitycheckCsetStructurecolDatacolData<-colDataMapcolDataMap<-colIDscollect_fn_paramscolMetacolnames<-.immutableconnectivityScoreCoreSetCoreSet2cosinePermcurationcuration<-datasetTypedatasetType<-dateCreateddateCreated<-drop_fn_paramsdrugSensitivitySigendoaggregatefeatureInfofeatureInfo<-fNamesfNames<-getInternguessMappinggwcidColsimmutableis_optim_compatibleis.immutableis.itemslapplyLongTableLongTableDataMappermake_optim_functionmccmDataNamesmDataNames<-mergeAssaysmetaConstructmetadatametadata<-metadataMapmetadataMap<-molecularProfilesmolecularProfiles<-molecularProfilesSlotmolecularProfilesSlot<-mutablenamename<-optimizeCoreGxpertNumberpertNumber<-phenoInfophenoInfo<-rawdatarawdata<-reindexrowDatarowData<-rowDataMaprowDataMap<-rowIDsrowMetarownames<-.immutablesampleInfosampleInfo<-sampleNamessampleNames<-sensitivityInfosensitivityInfo<-sensitivityMeasuressensitivityMeasures<-sensitivityProfilessensitivityProfiles<-sensitivityRawsensitivityRaw<-sensitivitySlotsensitivitySlot<-sensitivitySlotToLongTablesensNumbersensNumber<-showshow.immutableshowSigAnnotsubsetsubset.immutablesubset<-.immutablesubsetByFeaturesubsetBySamplesubsetByTreatmentsubsetTosummarizeMolecularProfilessummarizeSensitivityProfilestreatmentInfotreatmentInfo<-treatmentNamestreatmentNames<-treatmentResponsetreatmentResponse<-TreatmentResponseExperimentTREDataMapperupdateObjectupdateSampleIdupdateTreatmentId
Dependencies:abindaskpassbackportsbase64encbenchBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbitopsbslibBumpyMatrixcachemcaToolscheckmatecliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrDTevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalsamagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmeopensslpianopillarpkgconfigprofmempromisespurrrR6rappdirsRColorBrewerRcpprelationsrlangrmarkdownS4ArraysS4VectorssassscalessetsshinyshinydashboardshinyjsslamsnowSnowballCsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevisNetworkwithrxfunxtableXVectoryamlzlibbioc
CoreGx: Class and Function Abstractions for PharmacoGx, RadioGx and ToxicoGx
Rendered fromcoreGx.Rmdusingknitr::knitron Jun 19 2024.Last update: 2022-06-23
Started: 2021-05-20
The TreatmentResponseExperiment Class
Rendered fromTreatmentResponseExperiment.Rmdusingknitr::rmarkdownon Jun 19 2024.Last update: 2022-06-23
Started: 2022-06-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convenience function for converting R code to a call | . |
| Convert a LongTable assay into a BumpyMatrix object | .assayToBumpyMatrix |
| Curve fitting via 'stats::optim' L-BFGS-B with fall-back grid/pattern search if convergence is not achieved. | .fitCurve2 |
| Convert LongTable to gDR Style SummarizedExperiment | .longTableToSummarizedExperiment |
| [ LongTable Method | [,LongTable,ANY,ANY,ANY-method |
| [[<- Method for LongTable Class | [[<-,LongTable,ANY,ANY-method |
| Select an assay from a LongTable object | $,LongTable-method |
| Update an assay from a LongTable object | $<-,LongTable-method |
| Functional S4 API for aggregation over a 'data.table' object. | aggregate,data.table-method |
| Functional API for aggregation over a 'LongTable' or inheriting class | aggregate,LongTable-method |
| Functional API for data.table aggregation which allows capture of associated aggregate calls so they can be recomputed later. | aggregate2 |
| Calculate an Adaptive Matthews Correlation Coefficient | amcc |
| Coerce a 'LongTable' to a 'TreatmentResponseExperiment' | as |
| Coerce from data.table to LongTable | as.long.table |
| Generic to access the assay columns of a rectangular object. | assayCols |
| Retrieve and assayIndex | assayIndex |
| Retrieve a set of assayKeys | assayKeys |
| Intercept assignment operations for "immutable" S3 objects. | $<- $<-.immubtale, $<-.immutable assignment-immutable colnames<- colnames<-.immutable colnames<-.immutable, dimnames<- dimnames<-.immutable dimnames<-.immutable, names<- names<-.immutable rownames<- rownames<-.immutable rownames<-.immutable, subset<-.immutable subset<-.immutable, [<- [<-.immutable [<-.immutable, [[<- [[<-.immutable [[<-.immutable, |
| Build an assay table with an 'S4' object. | buildComboProfiles |
| Build an assay table with selected assay profiles for drug combinations | buildComboProfiles,LongTable-method |
| Build a LongTable object | buildLongTable |
| LongTable build method from character | buildLongTable,character-method |
| LongTable build method | buildLongTable,data.frame-method |
| LongTable build method from list | buildLongTable,list-method |
| Intercept concatenation for "immutable" class objects to return another "immutable" class object. | c.immutable |
| Search a data.frame for 1:'cardinality' relationships between a group of columns (your identifiers) and all other columns. | cardinality checkColumnCardinality |
| A function to verify the structure of a CoreSet | checkCsetStructure |
| Cleaveland_mut RadioSet subsetted and cast as CoreSet | clevelandSmall_cSet |
| Convenience method to subset the 'colData' out of the 'rawdata' slot using the assigned 'colDataMap' metadata. | colData,LongTableDataMapper-method |
| Convenience method to subset the 'colData' out of the 'rawdata' slot using the assigned 'colDataMap' metadata. | colData,TREDataMapper-method |
| Generic to access the row identifiers for an object. | colIDs |
| Collects all function arguments other than the first into a single list parameter. | collect_fn_params |
| Generic to access the column identifiers for a rectangular object. | colMeta |
| Function computing connectivity scores between two signatures | connectivityScore |
| List of 'deprecated' or 'defunct' methods in the 'CoreGx' R package. | CoreGx-defunct CoreGx-deprecated |
| CoreSet constructor | CoreSet |
| Accessing and modifying information in a 'CoreSet' | annotation annotation,CoreSet-method annotation<- annotation<-,CoreSet,list-method cellInfo cellInfo,CoreSet-method cellInfo<- cellInfo<-,CoreSet,data.frame-method cellName,CoreSet-method cellNames cellNames<- cellNames<-,CoreSet,list-method CoreSet-accessors curation curation,CoreSet-method curation<- curation<-,CoreSet,list-method datasetType datasetType,CoreSet-method datasetType<- datasetType<-,CoreSet,character-method dateCreated dateCreated,CoreSet-method dateCreated<- dateCreated<-,CoreSet,character-method dateCreated<-,CoreSet-method featureInfo featureInfo,CoreSet-method featureInfo<- featureInfo<-,CoreSet,character,data.frame-method featureInfo<-,CoreSet,character,DataFrame-method fNames fNames,CoreSet,character-method fNames<- fNames<-,CoreSet,character,character-method mDataNames mDataNames,CoreSet-method mDataNames<- mDataNames<-,CoreSet,ANY-method mDataNames<-,CoreSet-method molecularProfiles molecularProfiles,CoreSet-method molecularProfiles<- molecularProfiles<-,CoreSet,character,character,matrix-method molecularProfiles<-,CoreSet,character,missing,matrix-method molecularProfiles<-,CoreSet,missing,missing,list-method molecularProfiles<-,CoreSet,missing,missing,list_OR_MAE-method molecularProfiles<-,CoreSet,missing,missing,MutliAssayExperiment-method molecularProfilesSlot molecularProfilesSlot,CoreSet-method molecularProfilesSlot<- molecularProfilesSlot<-,CoreSet,list-method molecularProfilesSlot<-,CoreSet,list_OR_MAE-method molecularProfilesSlot<-CoreSet,MultiAssayExperiment-method moleculerProfilesSlot,CoreSet-method name name,CoreSet-method name<- name<-,CoreSet,character-method name<-,CoreSet-method pertNumber pertNumber,CoreSet-method pertNumber<- pertNumber<-,CoreSet,array-method phenoInfo phenoInfo,CoreSet,character-method phenoInfo<- phenoInfo<-,CoreSet,character,data.frame-method phenoInfo<-,CoreSet,character,DataFrame-method sampleInfo sampleInfo,CoreSet-method sampleInfo<- sampleInfo<-,CoreSet,data.frame-method sampleName,CoreSet-method sampleNames sampleNames,CoreSet-method sampleNames<- sampleNames<-,CoreSet,character-method sampleNames<-,CoreSet,list-method sensitivityInfo,CoreSet,character-method sensitivityInfo,CoreSet,missing-method sensitivityInfo,CoreSet-method sensitivityInfo<-,CoreSet,data.frame-method sensitivityInfo<-,CoreSet,missing,data.frame-method sensitivityMeasures,CoreSet-method sensitivityMeasures<-,CoreSet,character-method sensitivityProfiles,CoreSet-method sensitivityProfiles<-,CoreSet,data.frame-method sensitivityRaw,CoreSet-method sensitivityRaw<-,CoreSet,array-method sensitivitySlot sensitivitySlot<- sensitvityInfo<-,CoreSet,character,data.frame-method sensNumber sensNumber,CoreSet-method sensNumber<- sensNumber<-,CoreSet,matrix-method treamentResponse<-,CoreSet,list-method treatmentInfo treatmentInfo,CoreSet-method treatmentInfo<- treatmentInfo<-,CoreSet,data.frame-method treatmentNames treatmentNames,CoreSet-method treatmentNames<- treatmentNames<-,CoreSet,character-method treatmentResponse treatmentResponse,CoreSet-method treatmentResponse<- treatmentResponse<-,CoreSet,list_OR_LongTable-method treatmentResponse<-,CoreSet,LongTable-method |
| CoreSet - A generic data container for molecular profiles and treatment response data | .CoreSet CoreSet-class |
| Utility methods for a 'CoreSet' object. | CoreSet-utils subsetByFeature subsetByFeature,CoreSet-method subsetBySample subsetBySample,CoreSet-method subsetByTreatment subsetByTreatment,CoreSet-method |
| Make a CoreSet with the updated class structure | CoreSet2 |
| Cosine Permutations | cosinePerm |
| Accessing and modifying data in a 'DataMapper' object. | DataMapper-accessors rawdata rawdata,DataMapper-method rawdata<- rawdata<-,DataMapper,ANY-method |
| An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object | .DataMapper DataMapper-class |
| Drop parameters from a function and replace them with constants inside the function body. | drop_fn_params |
| Perform aggregation over an S4 object, but return an object of the same class. | endoaggregate |
| Functional API for endomorphic aggregation over a 'LongTable' or inheriting class | endoaggregate,LongTable-method |
| Example LongTableDataMapper | exampleDataMapper |
| Retrieve the specified item from object internal metadata. | getIntern |
| Generic for Guessing the Mapping Between Some Raw Data and an S4 Object | guessMapping |
| Guess which columns in raw experiment data map to which dimensions. | guessMapping,LongTableDataMapper-method |
| GWC Score | gwc |
| Generic to access the unique id columns in an S4 object used to | idCols |
| Constructor for "immutable" S3-class property | immutable immutable_list-class is.immutable print.immutable show.immutable |
| Check whether a function signature is amenable to optimization via 'stats::optim'. | is_optim_compatible |
| Get the types of all items in a list | is.items |
| lapply lapply method for 'MultiAssayExperiment' | lapply,MultiAssayExperiment-method |
| A class union to allow multiple types in a CoreSet slot | list_OR_LongTable-class |
| LongTable constructor method | LongTable |
| Accessing and modifying information in a 'LongTable' | LongTable-accessors |
| Constructor for the 'LongTableDataMapper' class, which maps from one or more raw experimental data files to the slots of a 'LongTable' object. | LongTableDataMapper |
| Accessing and modifying data in a 'LongTableDataMapper' object. | assayMap,LongTableDataMapper,List-method assayMap,LongTableDataMapper,list-method assayMap,LongTableDataMapper-method assayMap<-,LongTableDataMapper,List-methhod assayMap<-,LongTableDataMapper,list-method assayMap<-,LongTableDataMapper,list_OR_List-method colDataMap,LongTableDataMapper-method colDataMap<-,LongTableDataMapper,list_OR_List-method colDataMap<-LongTableDataMapper,List-method LongTableDataMapper-accessors metadataMap,LongTableDataMapper-method metadataMap<-,LongTableDataMapper,list_OR_List-method metadataMap<-,LongTableDataMapper-method rawdata,LongTableDataMapper-method rawdata<-,LongTableDataMapper,list-method rowDataMap,LongTableDataMapper-method rowDataMap<-,LongTableDataMapper,list-method rowDataMap<-,LongTableDataMapper,list_OR_List-method rowDataMap<-LongTableDataMapper,List-method |
| A Class for Mapping Between Raw Data and an 'LongTable' Object | .LongTableDataMapper LongTableDataMapper-class show,LongTableDataMapper-method |
| Takes a non-primitive R function and refactors it to be compatible with optimization via 'stats::optim'. | make_optim_function |
| Compute a Mathews Correlation Coefficient | mcc |
| Merck Drug Combination Data LongTable | merckLongTable |
| Merge assays with an 'S4' object. | mergeAssays |
| Endomorphically merge assays within a 'LongTable' or inheriting class | mergeAssays,LongTable-method |
| Generic for preprocessing complex data before being used in the constructor of an 'S4' container object. | metaConstruct metaConstruct,LongTableDataMapper-method metaConstruct,TREDataMapper-method |
| Getter method for the metadata slot of a 'LongTable' object | metadata,LongTable-method |
| Setter method for the metadata slot of a 'LongTable' object | metadata<-,LongTable-method |
| Remove the "immutable" S3-class from an R object, allowing it to be modified normally again. | mutable |
| NCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset | nci_TRE_small |
| A helper method to find the best multithreading configuration for your computer | optimizeCoreGx |
| Generic method for resetting indexing in an S4 object | reindex |
| Redo indexing for a LongTable object to remove any gaps in integer indexes | reindex,LongTable-method |
| Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata. | rowData,LongTableDataMapper-method |
| Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata. | rowData,TREDataMapper-method |
| Generic to access the row identifiers from | rowIDs |
| Generic to access the row identifiers from | rowMeta |
| Generic function to get the annotations for a treatment response experiment from an S4 class | sensitivityInfo |
| sensitivityInfo<- Generic Method | sensitivityInfo<- |
| sensitivityMeasures Generic | sensitivityMeasures |
| sensitivityMeasures<- Generic | sensitivityMeasures<- |
| sensitivityProfiles Generic | sensitivityProfiles |
| sensitivityProfiles<- Generic | sensitivityProfiles<- |
| sensitivityRaw Generic Method | sensitivityRaw |
| sensitivityRaw<- Generic | sensitivityRaw<- |
| sensitivitySlotToLongTable Generic | sensitivitySlotToLongTable |
| Subset an immutable object, returning another immutable object. | $ $.immutable setOps-immutable subset, subset.immutable [ [.immutable [.immutable, [[ [[.immutable [[.immutable, |
| Show a CoreSet | show,CoreSet-method |
| Show method for the LongTable class | show,LongTable-method |
| Get the annotations for a 'Signature' class object, as returned by 'drugSensitivitysig' or 'radSensitivtySig' functions available in 'PharmacoGx' and 'RadioGx', respectively. | showSigAnnot |
| Subset method for a LongTable object. | subset,LongTable-method |
| Summarize molecular profile data such that there is a single entry for each sample line/treatment combination | summarizeMolecularProfiles |
| Summarize across replicates for a sensitivity dose-response experiment | summarizeSensitivityProfiles |
| TreatmentResponseExperiment constructor method | TreatmentResponseExperiment |
| Constructor for the 'TREDataMapper' class, which maps from one or more raw experimental data files to the slots of a 'LongTable' object. | TREDataMapper |
| Accessing and modifying data in a 'TREDataMapper' object. | assayMap assayMap,TREDataMapper,List-method assayMap,TREDataMapper,list-method assayMap,TREDataMapper-method assayMap<- assayMap<-,TREDataMapper,List-methhod assayMap<-,TREDataMapper,list-method assayMap<-,TREDataMapper,list_OR_List-method colDataMap colDataMap,TREDataMapper-method colDataMap<- colDataMap<-,TREDataMapper,list_OR_List-method colDataMap<-TREDataMapper,List-method metadataMap metadataMap,TREDataMapper-method metadataMap<- metadataMap<-,TREDataMapper,list_OR_List-method metadataMap<-,TREDataMapper-method rawdata,TREDataMapper-method rawdata<-,TREDataMapper,list-method rowDataMap rowDataMap,TREDataMapper-method rowDataMap<- rowDataMap<-,TREDataMapper,list-method rowDataMap<-,TREDataMapper,list_OR_List-method rowDataMap<-TREDataMapper,List-method TREDataMapper-accessors |
| A Class for Mapping Between Raw Data and an 'TreatmentResponseExperiment' Object | .TREDataMapper TREDataMapper-class |
| Update the 'CoreSet' class after changes in it struture or API | updateObject,CoreSet-method |
| Update the 'LongTable' class after changes in it struture or API | updateObject,LongTable-method |
